The Doctor's Forgotten Secret
by EmiQueenieArrow
Summary: This first part it just introduction to this character I made up. This was all inspired by a strange dream that I had so I hope you guys enjoy!
1. Chapter 1

The Doctor's Forgotten Secret

Part 1 The Queen's POV

I breathed in, smelling the fresh mountain air. I looked around me. Seeing the tops of mountains was amazing. I wasn't sure which range, but I guess right now it doesn't matter. I was floating at the cloud level. I smiled just before I rocketed off to the base. I landed on the runway.

I did a 360. It was crazy busy. There were people in dark uniforms giving orders and codes through their headsets. I saw an old car painted a bright red color. I spotted the man I was searching for. He was talking to a handsome fit man with dark hair. As I approached them the dark haired man stopped me before I could reach my target. I looked down at the ground.  
"I'm sorry miss, this is a restricted area." I looked up right into his eyes. His eyes bore deep into mine. Then I did the fun thing where I change my eyes from bright jade green to bright blood red. He flinched and lowered his arm.  
"Ah, there you are. Perfect timing. Excuse Agent Ward, he's well," Coulson sighed, "a by-the-book guy." He straightened his black suit.

"Is everyone on this team going to be like this?" I rose a couple feet in the air, my head cocked to the side, "Cause I don't think it's going to work out." The agent smiled and gently grabbed my wrist. He pulled me back to the ground before encasing me in his arms.  
"It's amazing to see you again Coulson," I said as I hugged Agent Coulson back.

He laughed and said, "Yeah, I missed all that fun time we spent together figuring out where that hammer came from." We released each other and I started walking up the ramp.

When I turned my back I heard Agent Ward ask Coulson, anger laced into his voice, "She got called in for the Thor situation and I didn't? Is because she can fly and change her eye color?" Coulson let out a soft laugh. He grabbed Ward's shoulder.

"It's definitely the eye thing." I walked up into the giant plane and seconds later Coulson was by my side. I was still marveling at how ginormous the inside was when Coulson interrupted my thoughts. "Should I tell them who you are and all of that?"

I pulled off my jacket and noticed a man messing around with a computer. He had brown hair that was a little curly and he looked like a child compared to the other agents. I approached him and asked, "Could you show me where to put this?" He took it from me.

"I can put it up for you miss." He said with his thick Irish accent. With that he turned to a girl with wavy brown hair and a gentle face and they walked off together. I returned to Coulson's side.

"I was thinking it would be fun to let them try and figure out who I am. Just to mess around with them a little. I'll tell them soon enough though." I smiled at Coulson before following him up a set if stairs.

We reached the top level of the plane. I sat down on the big couch. Agent Ward offered me a bottle of water. I smiled and thanked him. I took a couple sips before I grabbed a coaster and put it down. "See people, that's all I ask you to do." Coulson applauded, "Anyways, onto business. First let me introduce you to the team. You've already met Agent Ward. Your coat racks name is  
Fitz, and the girl that is next to him is Simmons. The girl on the cell phone is Skye and the pilot is Agent Melinda May."

"Hi everyone. It's nice to meet you all," I waved as I stood up. "Skye? Could you help me find a uniform?" I smiled and followed her to a small room. There were racks upon racks of uniforms, most of them the same. Almost all of them had the eagle looking emblem. I found a plain black shirt and put it on. I then found some black pants, a khaki pocketed strap, and combat boots. As I was putting on my uniform I talked to Skye.

"You a new recruit or something?"

"I'm a consultant. I'm not really an agent, although I'm working on it."

"Am I making you nervous? I haven't done anything scary yet."

She raised an eyebrow.

"Yeah, I said yet. I am pretty scary I'm not going to lie." I pulled one of the fingerless gloves out of my old jeans and put it on.

"Who are you?"

"I'm leaving that to all of you." I pulled out my other glove and put it on. I walked out of the door and wandered around the plane. I ended up in a lab. There were tools and beakers everywhere. I could smell something sterile, like a hospital. I could also smell something explosive. I sat on the stool right next to Simmons. She was saying something about the rock she was looking at.

"Can I see it?" She nodded and handed the rock to me. "Fourth moon of Centsatforlom, the Aposantel district. Looks like a chunk of normal rock, but it's not. I recommend not putting it in fire."

"Wha... What happens if I do?" She dropped the rock on her work table.

"It could blow up the plane, and America, and this half of the universe. I think you should probably drop it in the Arctic Ocean, not the warmest place so it should be fine." She took the rock to a freezer and locked it.

"Oh, please tell me you're not listening to her Simmons."

I raised an eyebrow as I looked at Fitz. "Oh and what do you know about intergalactic rocks? What are you working on?"

He looked down and shook his head. "Some new drones. I can't get them to fly and I'm starting to get frustrated." I held out my hand and he put the little metal bug into my hand.

"It won't fly if you don't charge the antigravity and rewrite the programming, and you know it's not bad to just tune it up." I pulled out my own tool, my prized possession from my home. I fixed the bug and handed it to Fitz. He about dropped it twice but finally put it safely on his table.

"I would love if you could tell me where you learned that." Fitz crossed his arms and watched me. "What was that thing that you used on my little friend?"

I laughed. "This? Oh, well, it's very very complex." I studied his face. "Oi, I would tell you but it's kind of a secret. Anyways, you two seriously don't put that rock in fire. I'm not messing around." I walked up a staircase and found myself in the living area that I met everyone in.

I saw Agent Ward studying some files. "You looked, well... Frustrated." He looked at me. I was standing against the doorframe. I watched his eyes wander up and down my body.

"That's enough of that." I sat beside him and leaned my head over the back of the couch.

"Uh, right. I can't figure out this case. It's very confusing. It's about the Royal Hope Hospital in London. People said it started raining backwards and it disappeared. It came back in a matter of time, but I have no idea how."

I pulled my head back up. "It's back. That's the good part. Don't stress too much about it. It will come to you eventually," I said with an accidental sigh.

"You make it sound as if you know exactly what happened." He cleaned up the papers and put them back into the folder.

"I never said I didn't." I leaned over to look at some extra papers on the table.

"Okay, for real who are you? Where did you come from."

"I told Skye the same thing I'm about to tell you. Figure it out yourself. I'm sure I'll do something weird then I'll probably have to explain myself." I smiled.

"Coulson wants to see you." I turned and watched May walk away. I had to fly to keep up with her brisk pace. She opened the door to his office. Once I entered she slammed the door shut. He looked up and sighed.

"I can see you haven't changed your style." He shook his head at my black button down shirt with a khaki strap going across my body holding my important stuff, black pants, and combat boots. I pulled at my black fingerless gloves.

"Can't help it. I haven't have time to figure out a new style for this situation. If I remember clearly I've been in jeans and old beat up Converses for the past year."

"That doesn't bother me, but you look like you're going to a funeral. Honestly. Your black hair isn't helping."

I shrugged and put my pin straight hair in a pony tail. "How about instead of trashing how I look you tell me what you want." I said with an annoyed tone.

"I've known you for a while and you do great work. You are also one of the best judges of character. Can we trust this team?"

"Everyone seems fine, but Skye is the only problem. I think she sensed that I was observing her. She acted extremely nervous."

"I've had my own suspicions but I just ignored it. Thank you for your input." I gave him a two fingered salut.

"Okay well, what did you need me for all the sudden? I know you didn't just feel like working with me again."

"S.H.I.E.L.D. needs you. We need you knowledge and your training. One mission, and you go back to running around and playing around with people."

"Fine. But it better happen soon. S.H.I.E.L.D. is much too serious for me."


	2. Chapter 2

The Doctor's Forgotten Secret

Part 2 The Queen's POV

"Oi, Ward, we get to go into the field together."

Without missing a beat he raised his head and said, "I'm dead." I flashed a color change at him and he shook his head. I sat in the lounge chair across from him and laid my head back. I closed my eyes and imagined home. My thoughts were interrupted by a horrible sound. I saw Simmons and Fitz had entered the room. They turned on the radio and played awful music with so much added to the voice it hurt my head. I put my hands over my ears and lowered my head. I took out my sonic screwdriver and pointed it at the radio. It went up into a display of sparks. Skye, May, and Coulson ran in after hearing the sparks.

Ward looked at me angrily. "What are you doing? Tell us who you are, now."

"Just drop it guys." I quieted Coulson's order with my hand.

"I have a feeling I should just tell you now. My name is The Queen, and I'm not from here."

Skye cut me off. "Queen? Of what?"

"No where. I'm just know as The Queen, or Queenie. I'm not human if you haven't noticed yet. I'm a Time Lord from the plant Gallifrey."

This time is was May who interrupted me. "You look completely human there is no way you're alien."

"I have two hearts. I can also regenerate into new bodies if the old one is too... damaged. This is already my 4th body and I'm still very young."

This was new information to Agent Coulson. "Does that mean you can't die? How old are you exactly?"

"I can die, if I don't regenerate in time. Or I could choose to not regenerate. Once I'm dead, I'm dead. Now my age is going to shock you so be prepared. Ready?" The whole room nodded. "I'm 702 years old." Fitz, Simmons, and Skye's jaws dropped. The other 3 didn't react. "My race was a time and space traveling race. We were a great race. Smart, strong. There were lots of words to describe us."

"Past tense. What happened?" May looked deep in my eyes and by habit they changed colors. "Also, do all Time Lords have powers like yours?"

"No other Time Lords had powers like mine. When we are children, only 8 years old, they take us to look at time itself. Some go mad. Most go on as normal. But when I looked at it part of the vortex jumped out at me and into my body. It jumped back into the rest of the vortex. After that I had powers like flight, strength, my lightning, and my amazing sword."

"Show them the sword thing," Coulson sounded like a child getting their first dog. I smile toward the ground and reached out toward the table. I slammed my hand on the table and slowly brought it back. As my hand rose a long silver sword appeared. Once the blade was two feet long, the handle appeared and it stopped growing. I grabbed it and twirled it on my fingertips.

"Can you mix your sword and lightning abilities?" Simmons started inspecting my sword.

"Yes, but I don't need the sword to use lightning. The sword just makes it more affective. And it looks cooler. Move back." I slammed the sword into the ground and it purred to life with lightning. When I pulled it up the lightning lit up the whole cabin. I balanced it on its tip and brought my hand down slowly. When the whole sword disappeared every person in the room had their jaw on the floor, even Ward.

I ignored them and kept telling the history of my powerful race. "The fall of the Time Lords was choice that a Time Lord had to make. He killed all of the Time Lords to kill all of the Daleks. They are the race that tried taking over time. It was the Time War. I fought in it. I was lucky enough to escape what the others had to suffer. I was in a smaller battle farther away but I still saw my people die. All of them. Gallifrey destroyed. I took care of the Dalek on my ship and wandered around until I found Earth. I can only guess the brave Time Lord is dead but I refuse to stop looking.

"That's when I met Coulson and got recruited for S.H.I.E.L.D. But soon after the Thor incident I left. And now I'm back."


	3. Chapter 3

The Doctor's Forgotten Secret

Part 3 The Queen's POV

I sat up suddenly. I could feel cuts all over my body. I looked around at the wreck. Our plane had definitely hit the ground. There was glass everywhere. The tables and chairs were charred. I grabbed my head. I remembered telling the story of the Time Lords and now our plane was on the ground. My thoughts were interrupted when I felt a sensation that I couldn't even label as pain or relief. I tried standing. I was slowly rising to my feet, but before I could I felt like my body was being ripped in half. My vision went blurry and I about fell back to the ground when I felt two strong arms grab me.

"Whoa, hold on there." Ward lowered me back to the ground. I looked around. I felt Ward move to check on everyone. I could see everyone except for Coulson. I turned and looked behind me. I still didn't see him. Slowly, everyone came back to the world.

The next feeling I got was a familiar feeling, but still strange. I felt my breathing increase. I felt my mouth open, but I didn't feel anything coming out. I looked up at the team. All of their eyes were looking right at me. "Queen, whats wrong?" I felt someone touch my arm. I saw Fitz looking at me. His face was covered with fear but his eyes suggested concern. I pulled away from him.

"I'm..." I couldn't continue my sentence. A new wave of sensations rolled through my body. My breathing stopped and started again. Simmons and Skye started reaching for me.

"No one touch her. Remember she told us what happens when she's hurt or dying." I heard Coulson's soft voice right next to my head.

Skye covered her mouth. Agent May, who was looking very serious as usual whispered, "She's regenerating." I got to my feet quickly. I could feel a wave of relief from the pain. My eyes closed, welcoming this warmth. When I opened them again I saw them still staring.

"I was able to heal. I didn't regenerate all the way. Now Coulson, are you hurt anywhere else besides your arm?" He shook his head. "Good. Ward, wrap it. I'll take care of everyone else."

Thirty minutes later we were talking to Nick Fury. He kept looking at Skye with his eye. There were people rummaging through the wreck, looking for what sparked the explosion. Skye was staring at her bandaged hands, and she looked mad.

Shortly after the crash we discovered we crashed near a farm, not far from London. "Well, it works out. The man we are looking for is in London. Ward and Queen are in pretty good shape for the most part. We are still going to find him as planned. You two have until tomorrow to prepare." We nodded. We turned to get our equipment for the fast approaching mission. Ward got into a S.H.I.E.L.D. Mobile Armory. There were rows of big guns. The back wall was all knives and hand guns. Ward offered me two knives.

"No thanks. I already have my sword." Ward shrugged. He reached for a small hand gun and threw it at me. I let it fall to the ground at my feet.

"Queen, put it in your holster." He waited for me to pick it up.

"Do you see a holster?" He looked at me before answering with a simple no. "Never liked guns, never will. So don't ever put one near me ever again." He picked it up and slid both guns into his own hidden holster. I walked to Fitz and Simmons. They were both okay aside from small cuts and bruises.

"You two okay?" I saw Simmons tremble a little but other then that I got no response. "Oi, you lot. How are you feeling?" Fitz was the first to react. He shook his head. "I should have gotten an alert from my computers. No energy spikes, and no temperature spikes either."

"I'm still trying to figure that out too. No alerts, nothing. It's very strange." Simmons turned toward Fitz and they started talking about it. I turned and walked toward Coulson and Fury. I was reaching out to tap Coulson's shoulder when I stopped. I ran into the plane, into what was left of the common room. I turned over the charred couch and the blackened tables. I finally found what I was looking for. The remains of a cell phone. Skye's cell phone.


	4. Chapter 4

The Doctor's Forgotten Secret

Part 4 Queens POV

I held the small phone in my hand. I could see the way the screen had been torn open, the sides bent like a tree in a hurricane. This is what knocked us out of the sky. Another thought occurred to me. I ran into the empty lab. I opened the small freezer. I breathed a sigh of relief. The explosive space rock had been sparred by the flames. I shut the box and carried it, along with the cell phone, out to Coulson and Fury. I dropped the box onto the ground.

"It was Skye. Her phone exploded. Also, can you get this dropped into the Arctic Ocean by any chance?" I gestured to the box. Fury picked up the phone and looked at it.

"How did you figure out it was her?" He looked at me with not the slightest sign of any emotion. It made my thoughts slow down. I snapped out of it and told them my theory.

"I talked to Fitz and he said his computer didn't give any signal to a threat. No temperature spikes, no energy spikes, nothing. The only other person on this plane that could possibly override those codes is her. Her background with the Rising Tide gives me another reason to believe it was her." There was a tense silence as Fury thought it over.

"Get to the unmarked Jeep. You and Ward are to go to the hotel that the man is staying in. While you drive into London, Ward can give you the back ground about this guy. The address is already in the GPS." Without a second glance he walked back to his helicopter.

"Not very friendly is he?" I asked, slightly frustrated. I exhaled sparks from my mouth. Coulson just looked at me. "Okayyyy. Hey! Wait! You forgot the box!" I shouted after the super spy. Before I could finish my sentence two men grabbed the box and locked it into the small jet. "Oi, thanks boys!" I wiped some dirt onto my jeans then found the Jeep. I hopped in behind the wheel. Ward cautiously got into the passenger seat.

"Oh, come on. I might be a good driver."

He leaned his head to the side. "You've never driven a car before, right?"

"Nope, but I've been meaning to learn," I shook my head, "Hey. If I can fly a space ship I should be able to drive one of your daft machines."

Half an hour later we were in London, parked in a S.H.I.E.L.D operated garage. As we were grabbing our stuff from the back I looked at his face. This was the first time I really had a good look at his face. I quickly looked back at my bags before saying anything. "Well not bad for a first time driver." I said nervously.

He just shrugged. "I guess. Let's get to the hotel. We need to get to sleep." We started walking toward the hotel. We reached it in a matter of minutes but in the silence between us it felt like ages. Even though the hotel was huge and lit up I couldn't focus on it. All of the days activities had caught up with me and I found it rather difficult to keep upright. When we reached our room I hopped in the shower, hoping it would wake me up.

It really helped. When I saw a clean uniform, including my gloves sitting on the bed, I tried thinking of a good reason why I was here. I pushed the thought out of my mind and quickly dressed. I then joined Ward on the balcony.

"Thanks for getting my uniform and everything." I smiled at him.

"Yeah sure. Since there is only one bed, I'll just sleep on the couch." He rubbed his eyes with his hands. I could see his exhaustion on his face.

"Don't be ridiculous, you get the bed. And no protesting. Now go head in there. I need some time to think." He silently left my side and stepped inside. The lights clicked off and I was left in the dark. The lights of London were reflecting off the sky. I got a strange feeling that reminded me of Gallifrey. I shook it off and looked at the street below. I saw a van with three words painted in red on the side. It read, "The Queen is..." I looked but didn't see anything else.

I looked at it a little longer before stepping into the room, engulfed by the darkness. I laid on the couch and immediately fell asleep.


	5. Chapter 5

The Doctor's Forgotten Secret

Part 5 Queen's POV

Screaming. Fire. Explosions all around. My beautiful plant left in ruins. I could see the shards of ships left. Seeing my planet and life being destroyed and doing nothing to stop it was the most painful experience. I was busy watching my planet and when my guard was down they beamed a Dalek onto my large one person ship.

I felt the Dalek shoot me. I hit a button and it threw the bulky machine into space. My computers sensed it was gone and the doors shut. I was panting and sweating by then. I looked at my reflections in the panels lining the wall. I saw my blue eyes and blonde hair. I saw my face that I had been living with for 200 years. I felt the warm relief from the pain. It was comforting, I felt like everything would be okay. I checked my reflection again. I had my green eyes and straight black hair.

I got back into my seat. I looked at the destruction and devastation all around me. The Dalek ship I was fighting disappeared. But that wasn't my focus. My focus was the people. My whole race gone. The Time Lord that ended it all was nowhere in sight. I was hit with a crushing feeling of grief. A single tear rolled down my cheek. I knew I would never forget Gallifrey but I searched for a new planet. I searched for hundreds of years. I finally made it to the Earth but it took me a long time. A couple of years I could only guess. I landed in the middle of a desert. I lived out of my ship and away from any humans.

I planned on living like this for a while, at least until my supplies were depleted. My plans were gone with wind when I was surrounded by black helicopters and vans. I ran and as I did I blew up my ship. I knew the technology was too advanced for this time. A man in a suit and tie caught up to me and tackled me. I tried to fight but the heat was weakening me. It was just too hot for me. He put the cold strong metal cuffs on me.

I hung my head low. I was captured by a human. But I didn't try to run. I didn't fight. I really couldn't. I didn't even realize how far we were from his friends. They were in sight again when I gave up. I fell to my knees. My face was caked with dust and dirt. Tears streaked my nasty sun burned cheeks.

I expected for the agent to pull at my cuffs, try to get me up. But instead he just sat down next to me. He started talking about all the places he has been. He talked of the great people he meet recently. And he talked about the battles he has won. My tears subsided and I looked at the man. He was looking at me expectantly. I stood up and walked toward group of vehicles.

He sighed and followed. Just before we reached the vans, he took off the hand cuffs. "Make a choice kid. You can work for S.H.I.E.L.D or you can run." I looked toward the sky. I thought for two seconds before making the decision to join. I sat in a van feeling the air conditioner cool me off. I had my strength regained. I was really talkative to that one agent. I talked as a woman cleaned off my face.

I finished talking and he cleared his throat. "S.H.I.E.L.D requests your assistance with something." That's when I started working with Coulson.


	6. Chapter 6

The Doctor's Forgotten Secret

Part 6 The Queen's POV

I woke up at dawn. I watched the sun rise above the buildings. After my morning fog dissipated, I smelled something delicious. There was a cart with tea waiting next to me. I drank a cup of tea, thinking about my past.

"You talk in your sleep you know." Ward sat down beside me. I raised an eyebrow and wrapped myself in a blanket.

"What did I speak of?" I asked, curious of what I could have revealed to him.

"I didn't catch it all, but I did get something about Gallifrey, Dalek, Time Lords, regeneration, and pain." I put my tea cup down on the cart. We sat in silence. I got up and ready for the day to come. I exited the bathroom and saw Ward still sitting on the couch.

"What was it like to see your people die? See your planet destroyed?" His question stopped me in my tracks. I took a deep breath. I turned to him.

"It's more painful than anything I have ever experienced. Worse than death. You feel helpless and useless. I'm here to make sure you never feel that." I finished my oath. He studied my face and simply nodded. He got ready next. "So this terrorist is three floors above us?"

"Correct. We just need to find out where his base is. That's all we need to do. We aren't supposed to engage him." I nodded and saluted him.

I fixed my boots. "Got it chief." We got the signal in our ear pieces. We headed for the lobby. We got there and realized how difficult it would be to spot him. There were tons of people. They were swarming. We watched the lifts from the desk, acting like were waiting for service. The target stepped out of the lift. Ward tapped my side and signaled with his eyes.

We followed him out onto the street. He had a girl and two body guards with him. The guard turned and looked at us. He said something in Russian and they raced down the street. Ward and I kicked it into high gear.

I translated in my head "He recognized you from somewhere!"

"I've probably arrested him before." Ward replied. We raced by a park. Then I heard it. I stopped running and stared at the park.

Ward grabbed my arm and tried pulling me back into the chase. "What are you doing? We have to follow him!"

I turned to face Ward. "Just shoot him like you were planning to do all along." Ward shook his head and pulled out a gun. He shot a tracker on the heel of his guards boot. They keep running through the street.

"Why did you guys stop?" I heard May yelling through the ear piece but it was just back ground noise. I walked into the park. I knew I heard correctly. It was a sign of hope. A sign of home. Then my blood boiled with anger.

I ran up to the blue police box. I ran my hand over the wood. I felt every single grain of the wood. I moved my fists to the door. I started banging and screaming. "Let me in! I know you're in there!" I keep banging. I saw people staring but I didn't care. When no one opened the door I pulled out my sonic screwdriver and opened it myself. Ward tried to follow me but I shut the door before he could get in. I stormed up the ramp onto a platform.

There was a man in a suit and a pair of beat up Converse. I paused in front of him. When I kicked him square in the chest, he flew back four feet. I heard a woman gasp behind me. I knew my eyes were bright red. She saw them and flinched back.

"Who is this? Is this an old girlfriend or companion?" She gasped, "This is your wife, isn't it?" I slammed my hand onto the control panel and my sword appeared. I pointed it inches from her throat.

"Shut... Up!" She let out a little whimper and closed her mouth. I saw the man sit up and rub the back of his head. His face read confusion. As I crouched beside him, I pushed him back onto the ground. "You left me behind. You didn't even look for me. You just left. You finished it and left. You just left me behind to go play hero, didn't you?"

His eyes widened and he stood up. He fell into a chair. I stayed in my crouching position, staring at the spot he was seconds before.

The Doctor's POV

The girl just stormed into the TARDIS. I didn't know who she was or how she got in. All I know is that she can kick hard. After she spoke, I knew her eye color from somewhere. It hit me like a freight train. I tried to stand but I just collapsed into my chair. I was shocked. I focused on the girl, still crouched next to where I was a short time before. Donna slowly approached me.

"Doctor, who is that?" She asked softly.

Without moving, I answered her question. "It's the Queen. And I've made a horrible mistake."


End file.
